Silva 138.1, which database do I download? Ref NR 99 or Ref?

[Nicholas_Bokulich]

Hi @DannyBoi97,
Just to add to @Mehrbod_Estaki's excellent advice:

@DannyBoi97

I am trying to download Silva 138.1 from this link here: ARB files.

Note that if you are trying to use these files with QIIME 2 (or many other bioinformatics tools) the SILVA files need to be reformatted somewhat significantly to be compatible. Fortunately, we have a QIIME 2 plugin for that, and a tutorial here:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…

Though the SILVA 138 sequences and taxonomy (processed using this plugin) are also available on the QIIME 2 data resources page:
https://docs.qiime2.org/2020.11/data-resources/

That's 138, though, not 138.1 yet, so if you want to use 138.1 with QIIME 2 for now we recommend following that RESCRIPt tutorial... the get-silva-data method will grab and process the 138.1 files by default.